Reactions, pathways and curation

Reactions

The basic unit of Reactome is a reaction, which is defined as any molecular event; including binding, phosphorylation, biochemical catalysis, molecular transport and spontaneous molecular events. These reactions can involve any biological molecule, but are typically proteins and small molecules (chemical compounds). Figure 2 shows examples of reactions on the Reactome website.

Pathways

A pathway is defined as a series of connected reactions, with each individual reaction considered as a single step in the pathway. These are represented as pathways in detailed molecular diagrams. Examples of pathways include immune system signalling, the cell cycle and apoptosis. In Reactome, we create pathways using reactions as building blocks. Reactions are interconnected based on biological relevance resulting in the formation of pathways. Figure 3 shows examples of various pathways and reaction representations in the Reacome website.

Curation

The key aspects of Reactome content are quality and attribution. Pathways are written by expert biologists and independently peer-reviewed before being included in the database. Reactions always cite scientific literature that experimentally verifies the described event. These manually curated human pathways are used as templates to computationally infer equivalent pathways in other species, including most commonly used model organisms. More details of the curation process will be presented later in this course.

To learn more about exploring pathways in Reactome have a look at our companion course Reactome: Exploring biological pathways.